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Open AccessArticle

A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton

1
Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
2
Anyang Institute of Technology, Anyang 455000, Henan, China
*
Author to whom correspondence should be addressed.
Genes 2019, 10(10), 829; https://doi.org/10.3390/genes10100829
Received: 14 September 2019 / Revised: 16 October 2019 / Accepted: 18 October 2019 / Published: 21 October 2019
(This article belongs to the Special Issue Selection Methods in Plant Breeding: From Visual Phenotyping to NGS)
Millions of hectares of land are too saline to produce economically valuable crop yields. Salt tolerance in cotton is an imperative approach for improvement in response to ever-increasing soil salinization. Little is known about the genetic basis of salt tolerance in cotton at the seedling stage. To address this issue, a genome-wide association study (GWAS) was conducted on a core collection of a genetically diverse population of upland cotton (Gossypium hirsutum L.) comprising of 419 accessions, representing various geographic origins, including China, USA, Pakistan, the former Soviet Union, Chad, Australia, Brazil, Mexico, Sudan, and Uganda. Phenotypic evaluation of 7 traits under control (0 mM) and treatment (150 mM) NaCl conditions depicted the presence of broad natural variation in the studied population. The association study was carried out with the efficient mixed-model association eXpedited software package. A total of 17,264 single-nucleotide polymorphisms (SNPs) associated with different salinity stress tolerance related traits were found. Twenty-three candidate SNPs related to salinity stress-related traits were selected. Final key SNPs were selected based on the r2 value with nearby SNPs in a linkage disequilibrium (LD) block. Twenty putative candidate genes surrounding SNPs, A10_95330133 and D10_61258588, associated with leaf relative water content, RWC_150, and leaf fresh weight, FW_150, were identified, respectively. We further validated the expression patterns of twelve candidate genes with qRT-PCR, which revealed different expression levels in salt-tolerant and salt-sensitive genotypes. The results of our GWAS provide useful knowledge about the genetic control of salt tolerance at the seedling stage, which could assist in elucidating the genetic and molecular mechanisms of salinity stress tolerance in cotton plants. View Full-Text
Keywords: cotton; genome-wide association study (GWAS); SNPs; salinity cotton; genome-wide association study (GWAS); SNPs; salinity
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Yasir, M.; He, S.; Sun, G.; Geng, X.; Pan, Z.; Gong, W.; Jia, Y.; Du, X. A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton. Genes 2019, 10, 829.

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